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Methods used to sequence the transcriptome often produce more than 200 million short sequences. We introduce StringTie, a… Expand TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which… Expand Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript… Expand Brain development and function depend on the precise regulation of gene expression. However, our understanding of the complexity… Expand RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA… Expand RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this… Expand We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is… Expand Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms… Expand We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions… Expand The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide… Expand